LOCUS       NZ_CP096217             3274 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Enterococcus faecium strain UCH1 plasmid pUCH1-6, complete sequence.
ACCESSION   NZ_CP096217
VERSION     NZ_CP096217.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27725314
            Assembly: GCF_023204955.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3274)
  AUTHORS   Enroth,T.J., Kirsch,J.M., McCollister,B.D., Johnson,C.N. and
            Duerkop,B.A.
  TITLE     Enterococcus faecium UCH1
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3274)
  AUTHORS   Enroth,T.J., Kirsch,J.M., McCollister,B.D., Johnson,C.N. and
            Duerkop,B.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-APR-2022) Immunology and Microbiology, University of
            Colorado Anschutz Medical Campus, 12800 East 19th Ave, Aurora, CO
            80045, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: APR-2022
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: UCH1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 225.8x
            Sequencing Technology             :: Oxford Nanopore; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023204955.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 04:36:46
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,300
            CDSs (total)                      :: 3,209
            Genes (coding)                    :: 3,062
            CDSs (with protein)               :: 3,062
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 5, 5 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 5 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 51 of 147
            Pseudo Genes (incomplete)         :: 92 of 147
            Pseudo Genes (internal stop)      :: 37 of 147
            Pseudo Genes (multiple problems)  :: 28 of 147
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096217.1.
            Bacteria and source DNA available from Duerkop Lab, University of
            Colorado Medical School, Aurora, CO.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3274
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UCH1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pUCH1-6"
                     /geo_loc_name="USA"
                     /lat_lon="39.742630 N 104.842026 W"
                     /collection_date="2019"
                     /collected_by="Bruce McCollister"
     gene            join(<3273..3274,1..130)
                     /locus_tag="M0E25_RS16595"
                     /pseudo=""
     CDS             join(<3273..3274,1..130)
                     /locus_tag="M0E25_RS16595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002352765.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type III secretion system protein PrgN"
                     /name="type III secretion system protein PrgN"
     gene            356..1174
                     /locus_tag="M0E25_RS16340"
                     /old_locus_tag="M0E25_16340"
     CDS             356..1174
                     /locus_tag="M0E25_RS16340"
                     /old_locus_tag="M0E25_16340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305212.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_002305212.1"
                     /translation="MDTFQGTTFTVGNFKGGVGKTKIVSMLAYDNAMIRNRKTLIIDLD
                     PQANLTQVIARTFGITDIKTTITNGVANGELASSIIKVNENLDLLACDTSFRSFSAFAN
                     KHENELDQVTVLKKLLLPIKNNYQEIFIDVPPTISEFSDNAMAASDYSIISFQTAEESL
                     EGVNKYVNYQKFMVDRYDLDLQIIDIVPCMVEPNDDFDEEILEEAIEKYGTVVSKNLIH
                     YQKRLRRYSKIGIHLRKYKNGNFDQWDYKAHQVFINILAELDARQEFLNK"
                     /name="ParA family protein"
     gene            1193..1600
                     /locus_tag="M0E25_RS16345"
                     /old_locus_tag="M0E25_16345"
     CDS             1193..1600
                     /locus_tag="M0E25_RS16345"
                     /old_locus_tag="M0E25_16345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305214.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305774.1"
                     /translation="MPKDFDIPKMMENGEFEPLLPNNKRQDVKISGEYNFSNSALSNTR
                     NITLKKRGRPVSIPDKRNKVSVPKKISPALNSKLSILQDYMTELQSEKGRISFEKIVNT
                     LADSYIQHRLGVAKEEHIREEIQEEFEKLPK"
                     /name="hypothetical protein"
     gene            1920..3005
                     /locus_tag="M0E25_RS16350"
                     /old_locus_tag="M0E25_16350"
     CDS             1920..3005
                     /locus_tag="M0E25_RS16350"
                     /old_locus_tag="M0E25_16350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002352763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiator protein A"
                     /protein_id="WP_094850578.1"
                     /translation="MSTENQSQKMIIKNWGYKATNVYIEKYYKFPSFLIQNSKYSKMKD
                     SSKIAYMLFKNEFRRALHEKWIDDDGLLYLEFTQAELMDKLNCYQGKVKTILNELETYN
                     LISVVKGEFNPKTKKNEKNKYYLLQPEISADDLFIQNSFDDDLSETIDKSTSSRNAEIA
                     RREETAKTLDNTGNAEIARREKTAETLDNTGNAEIAQDYYINKSLDTKRHLKDTETDQL
                     QNQVLLDNFVEIMKEDSINTFVPEKVLSLIKTFSNTYEEAQQTVTTIHNAKHKAEELEK
                     TVVVYEELESYGIDADKGLYMTLLKAYQKQKTEKVNNLQNLIFVYVKNWFIEKAIAAKL
                     ANEQRETFNELPTVSTENWLE"
                     /name="replication initiator protein A"
     Typing          2599..3005
                     /name="rep_cluster_889"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtatatgat ctaagtcttg cttctagtat gaatatgacc gatgtatacg aaaagttatt
       61 aatactagaa aatgaatatg atcaattcaa ttcaaatcag cagcgaaaag taaagaaaca
      121 gatagactag aatagctatt ttcgaaaagc aatatttaag gtataagtta taccttaaat
      181 aataaaagta taagttatac cataaatata tatggtataa cttatacttt tattattaaa
      241 aaccgctata tccaaacgtt tttagatatt attatttaag ttatactttt aatgttgacc
      301 atttccgata tataagttat actttaatta tcaattaaag attgggagga tttacatgga
      361 tacttttcaa gggactacat ttacagttgg caattttaaa ggaggagtag gtaaaactaa
      421 gatagtcagc atgcttgctt atgacaatgc aatgataaga aatagaaaaa cgcttattat
      481 tgatttagac cctcaagcga acttaacaca agtcatagca agaactttcg gtataaccga
      541 tatcaaaacc actataacaa atggtgtcgc aaatggagaa ttagcaagta gtattattaa
      601 ggtaaatgaa aatcttgacc ttctggcatg tgacactagt tttcgatcat tctccgcttt
      661 tgctaataaa catgaaaatg aattagacca agttactgtc ttgaaaaaat tacttcttcc
      721 aataaagaac aattatcaag aaatatttat tgatgtacca ccaaccatta gcgaattttc
      781 cgataatgct atggcagctt cagactattc gataatttca tttcaaacag ctgaagaatc
      841 cttagaggga gtcaacaaat atgtaaatta tcaaaaattc atggtcgata gatacgatct
      901 tgatttgcaa attatagata ttgtaccttg tatggtagaa ccaaatgatg attttgatga
      961 agaaatccta gaagaagcaa ttgaaaaata cggaaccgtg gtatccaaaa atctcattca
     1021 ttatcaaaaa agattgagaa ggtattctaa aattggtata catttaagaa aatacaaaaa
     1081 tggaaatttt gatcaatggg attataaagc acaccaagta tttataaata ttttggcaga
     1141 actagatgct agacaagagt ttttaaataa ataataagga gttgcataag taatgcctaa
     1201 agattttgat attcctaaaa tgatggagaa tggtgaattt gagccattat tacccaataa
     1261 caaacgccaa gatgtgaaaa taagcggtga atataacttt agcaatagtg cattgagtaa
     1321 cacaagaaat attacattga aaaaaagagg ccgaccagtt tcaattcctg ataaaagaaa
     1381 caaggtatca gttcctaaaa agatctctcc ggcattaaat agcaaactct caattttaca
     1441 agactatatg acggagttac aaagtgaaaa agggagaatt tctttcgaaa aaattgttaa
     1501 tacattagca gactcatata tccagcatag actaggagta gcaaaagaag aacacataag
     1561 agaagaaata caagaagagt ttgaaaaatt accaaaataa ttttttttca tgcggtattc
     1621 aattaaagta taagttatac tagataaatg aatattaaag tataagttat acattaaata
     1681 tttaaggtat aacttaataa acaacgtgta aatttgcgat taaatcaaca ttataaaatt
     1741 attatttaaa gtataagtta tacattattt gtatttaaag tataacttat acttattttt
     1801 ttaatatata acttatacct taaatactga aagtgtttta ttcaccctta atacatggta
     1861 tagttcactt gttgaaaatc ctgaatatat acaagtttct aagaagaagg agaaatttaa
     1921 tgtctacaga aaatcaatct caaaaaatga taattaaaaa ttggggatat aaagcaacga
     1981 atgtttatat tgaaaaatat tataaatttc ctagtttttt aattcagaat tctaaatact
     2041 ctaaaatgaa agacagctca aaaatagcct atatgctttt taaaaatgaa tttcgtagag
     2101 ccttacatga aaaatggatc gacgatgatg gtctattata tttggaattt acacaagcag
     2161 aactaatgga caaattaaat tgctaccaag gcaaagtaaa aaccatttta aacgagttag
     2221 aaacatataa tttgatttca gtcgtaaaag gagaatttaa cccaaaaacg aaaaaaaatg
     2281 aaaaaaataa atactattta cttcaacctg aaataagtgc cgatgatctt tttattcaaa
     2341 attctttcga tgacgattta agcgaaacta ttgataaatc aacctcttct cggaatgcgg
     2401 aaatcgcacg tcgagaggaa actgctaaaa cccttgataa cactggaaat gcggaaatcg
     2461 cacgtcgaga aaaaacagct gaaacccttg ataacactgg aaatgcggaa atcgcacaag
     2521 attattatat taataaatct ttagacacta aaagacactt aaaagacact gaaacagacc
     2581 aattacaaaa tcaagttttg ctagataact tcgttgaaat catgaaagaa gacagcataa
     2641 acacatttgt accagaaaag gtattaagct tgataaaaac attttctaac acttacgaag
     2701 aagcccaaca aaccgtcacc acaatacaca acgcaaaaca taaagccgag gaacttgaga
     2761 agacggtagt tgtgtatgaa gaacttgaat cttacggaat tgatgcggat aaaggattat
     2821 atatgacgtt gctgaaagct tatcaaaaac aaaagactga gaaagtaaat aatttgcaga
     2881 atttgatttt tgtgtatgta aaaaactggt ttattgaaaa agctattgcg gcaaagcttg
     2941 caaacgaaca aagagaaaca tttaacgaat taccaacagt tagtacggaa aattggctag
     3001 agtagttgat aaaaagcgaa cactataaaa atgatcaatt ttaaattaga acttttttac
     3061 aattttaatt ttattacaaa tgttacaaat aaatagttat tattccggag tttttagatt
     3121 aaaagtttat gaaaacaatc acaaacgtag gttttaatgt cataatcgtt agatatttta
     3181 gttatttttc attcaaaaaa acagggaact agtgtttgca tatgtatttt tttgagttat
     3241 aataattcat gaagagaggt aattcactta ttta
//
